How does the custom css skin option work? The list on the options says "Custom (custom.css)", but I can't find that file in the plugin folder. I do find a "custom-sample.css". Is that the file I need to edit if I choose the custom skin? Or do I need to move it somewhere?

It works like wp-config-sample.php - you'll just want to rename custom-sample.css to custom.css and then you'll be good to go. The reason I don't include a custom.css is because then every time you update the plugin, your custom CSS would be overwritten :)

That is true, b-summers. It was written with the Pro version in mind, which would be updated via FTP and overwriting only those files that exist in the default install, so custom.css would remain intact. For now, you would need to manually backup and restore the custom.css file, though I'm working on automating that for when the Pro version includes automatic updates. Thanks for pointing that out though!

You could always add a custom stylesheet via your child theme, you'd just also need to enqueue it via your functions.php. There isn't a specific folder in the child theme that'll automatically get picked up, but it's an interesting idea to look into :)